https://github.com/okerew/biobridge
Biobridge is a Python library for simulating biological processes and systems also analyzing them, visualising them, and interacting with them.
https://github.com/okerew/biobridge
analysis biology biopython bridge c cpu database learning library linux machine macos python realtime simulation unix windows
Last synced: 4 months ago
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Biobridge is a Python library for simulating biological processes and systems also analyzing them, visualising them, and interacting with them.
- Host: GitHub
- URL: https://github.com/okerew/biobridge
- Owner: Okerew
- License: mit
- Created: 2025-02-11T18:50:58.000Z (12 months ago)
- Default Branch: main
- Last Pushed: 2025-09-28T09:49:56.000Z (4 months ago)
- Last Synced: 2025-10-02T04:27:13.914Z (4 months ago)
- Topics: analysis, biology, biopython, bridge, c, cpu, database, learning, library, linux, machine, macos, python, realtime, simulation, unix, windows
- Language: Python
- Homepage: https://pypi.org/project/biobridge/
- Size: 5.68 MB
- Stars: 6
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 
biobridge
[](https://youtu.be/NJjOs8crb50?si=crlh7BSLSodye2MS)
Biobridge is a Python library for simulating biological processes and systems also analyzing them, visualising them, and interacting with them.
## Installation
Firstly you need to install pyrosetta
Then install biobridge
```sh
pip install biobridge
```
## Usage
To use Biobridge in your project, import it for example:
``` python
from biobridge import *
# Create two proteins
protein1 = Protein("Protein A", "ACDEFGHIKLMNPQRSTVWY")
protein2 = Protein("Protein B", "YVWTSRQPNMLKIHGFEDCA")
# Define bindings for the proteins
protein1.add_binding("Site 1", "High")
protein2.add_binding("Site 3", "Medium")
# Create a cell with specific properties
cell1 = Cell(
name="Cell X",
cell_type="Epithelial Cell",
)
organelle = Mitochondrion(0.5, 100)
# Add organelles to the cell
cell1.add_organelle(organelle, quantity=10)
cell1.add_organelle(Organelle("Nucleus", 1), quantity=1)
cell1.add_organelle(Organelle("Ribosome", 100), quantity=100)
cell1.add_chromosome(Chromosome(DNA("ATCG" * 1000), "Chromosome 1"))
# Print cell details
print("Cell X Description:")
print(cell1)
```
## The notable functions are:
```python
from biobridge import *
Cell()
DNA()
RNA()
Protein()
Chromosome()
Environment()
Tissue()
System()
ImageAnalyzer()
Orchestrator()
Virus()
Infection()
SQLDNAEncoder()
SurgicalSimulator()
```
To see more examples how to use biobridge see the test files, biobridge works well with jupyter notebooks.
DO NOT USE THIS SOFTWARE FOR MEDICAL ANALYSIS OR ANY DIAGNOSIS, FOR THAT CONTACT A LICENSED MEDICAL EXPERT.